Gene annotation of the Fhb1 locus on the assembly of bread wheat variety Norin 61

<p>In the areas with wet climate of Eastern Asia, Fusarium head blight (FHB) is a major threat to bread wheat production. A source of FHB resistance (<em>Fhb1</em>) was identified in the Asian wheat germplasm and through classical breeding it was introduced in several varieties (https://doi.org/10.1186/s40066-017-0139-z ). The molecular determinant was identified as a deletion in an  histidine-rich calcium-binding-protein gene on chromosome 3BS. (https://doi.org/10.1038/s41588-019-0426-7). The allele is common in many East Asia wheat varieties, but not in the reference assembly Chinese Spring (CS). </p> <p>The whole-genome assembly of the Japanese variety Norin 61 allowed to confirm the sequence and structure of the haplotype surrounding <em>Fhb1</em>. Given the low amount of sequence conservation with CS at the locus, we noticed that the annotation based on projections of CS gene models (https://doi.org/10.1038/s41586-020-2961-x) did not identify all genes in the Norin 61 haplotype.</p> <p>To describe the complete set of coding regions in the <em>Fhb1</em> allele, we de novo annotated the Norin 61 ~340 kb <em>Fhb1</em> region with homology- and ab initio-based evidence. MAKER v2.31.9 was run on the Norin 61 genomic interval, with the Uniprot Liliopsida proteome, and the annotation from https://doi.org/10.1038/s41586-020-2961-x. Augustus was run with wheat as a species, and the output was parsed removing models that had &gt;40% similarity over &gt;50% of their length to TE proteins via BLASTP.</p> <p>Our annotation identified 70 protein-coding genes, 50 more than the ones identified by homology only.A deletion in the start codon (third exon) of <em>TaHRC</em> gene was confirmed as the causal mutaiton conferring resistance, and it was present in other vaireties having the same resistance.</p> <p>This resource highlights the importance of an appropriate characterization of the sequence in a non-reference genotype, especially when considering new variants with traits important for modern breeding programs.</p>